Mercurial > repos > galaxyp > openms_metaprosip
changeset 7:d06e5c4396d7 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d2b76821e22b13ed6e21795ac1b82446d8f594c6
author | galaxyp |
---|---|
date | Fri, 18 Aug 2017 13:57:26 -0400 |
parents | e6fb7acc98cc |
children | 4df3255d1c17 |
files | MetaProSIP.xml macros.xml |
diffstat | 2 files changed, 7 insertions(+), 5 deletions(-) [+] |
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--- a/MetaProSIP.xml Tue Aug 08 13:19:13 2017 -0400 +++ b/MetaProSIP.xml Fri Aug 18 13:57:26 2017 -0400 @@ -9,7 +9,9 @@ </macros> <expand macro="references"/> <expand macro="stdio"/> - <expand macro="requirements"/> + <expand macro="requirements"> + <requirement type="package" version="3.3.1">r-base</requirement> + </expand> <command>MetaProSIP #if $param_in_mzML: @@ -27,9 +29,9 @@ #if $param_in_featureXML: -in_featureXML $param_in_featureXML #end if -#if $param_r_executable: - -r_executable $param_r_executable -#end if + +-r_executable 'R' + #if $param_mz_tolerance_ppm: -mz_tolerance_ppm $param_mz_tolerance_ppm #end if @@ -133,7 +135,6 @@ <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/> <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/> <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/> - <param name="param_r_executable" type="data" format="txt" value="R" label="Path to the R executable (default: 'R')" help="(-r_executable) "/> <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/> <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/> <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
--- a/macros.xml Tue Aug 08 13:19:13 2017 -0400 +++ b/macros.xml Fri Aug 18 13:57:26 2017 -0400 @@ -6,6 +6,7 @@ <requirement type="package" version="15.12.15.2">xtandem</requirement> <requirement type="package" version="1.0">fido</requirement> <requirement type="package" version="2016.10.26">msgf_plus</requirement> + <yield/> </requirements> </xml> <xml name="stdio">